abund {pastecs} | R Documentation

## Sort variables by abundance

### Description

Sort variables (usually species in a species x stations matrix) in function of their abundance, either in number of non-null values, or in number of individuals (in log). The `f` coefficient allows adjusting weight given to each of these two criteria.

### Usage

    abund(x, f=0.2)
    ## S3 method for class 'abund':
    summary(abd)
    ## S3 method for class 'abund':
    plot(abd, n=abd$n, lvert=TRUE, lvars=TRUE, lcol=2, llty=2,
            all=TRUE, dlab=c("cumsum", "% log(ind.)", "% non-zero"),
            dcol=c(1, 2, 4), dlty, dpos=c(1.5, 20), ...)
    ## S3 method for class 'abund':
    lines(abd, n=abd$n, lvert=TRUE, lvars=TRUE, ...)
    ## S3 method for class 'abund':
    identify(abd, label.pts=FALSE, lvert=TRUE, lvars=TRUE, ...)
    ## S3 method for class 'abund':
    extract(abd, n=abd$n, left=TRUE)

### Arguments

`x` | A data frame containing the variables to sort according to their abundance in columns
`f` | Weight given to the number of individuals criterium (strictly included between 0 and 1; weight for the non-null values is `1-f`. The default value, `f=0.2`, gives enough weight to the number of non-null values to get abundant species according to this criterium first, but allowing to get at the other extreme rare, but locally abundant species
`abd` | An 'abund' object returned by `abund`
`n` | The number of variables selected at left
`lvert` | If `TRUE` then a vertical line separate the n variables at left from the others
`lvars` | If `TRUE` then the x-axis labels of the n left variables are printed in a different color to emphasize them
`lcol` | The color to use to draw the vertical line (`lvert=TRUE`) and the variables labels (`lvars=TRUE`) at left af the nth variable. By default, color 2 is used
`llty` | The style used to draw the vertical line (`lvert=TRUE`). By default, a dashed line is used
`all` | If `TRUE` then all lines are drawn (cumsum, %log(ind.) and %non-null). If `FALSE`, only the cumsum line is drawn
`dlab` | The legend labels
`dcol` | Colors to use for drawing the various curves on the graph
`dlty` | The line style to use for drawing the various curves on the graph
`dpos` | The position of the legend box on the graph (coordinates of its top-left corner). A legend box is drawn only if `all=TRUE`
`...` | additional graph parameters
`label.pts` | Do we have to label points on the graph or to chose an extraction level with the `identify()` method?
`left` | If `TRUE`, the n variables at left are extracted. Otherwise, the total-n variables at right are extracted

### Details

Successive sorts can be applied. For instance, a first sort with `f = 0.2`, followed by an extraction of rare species and another sort with `f = 1` allows to collect only rare but locally abundant species.

### Value

An object of type 'abund' is returned. It has methods `print()`, `summary()`, `plot()`, `lines()`, `identify()`, `extract()`.

### Author(s)

Philippe Grosjean (phgrosjean@sciviews.org), Frédéric Ibanez (ibanez@obs-vlfr.fr)

### References

Ibanez, F., J.-C. Dauvin & M. Etienne, 1993. Comparaison des évolutions à long terme (1977-1990) de deux peuplements macrobenthiques de la baie de Morlaix (Manche occidentale): relations avec les facteurs hydroclimatiques. J. Exp. Mar. Biol. Ecol., 169:181-214.

### See Also

`escouf`

### Examples

    data(bnr)
    bnr.abd <- abund(bnr)
    summary(bnr.abd)
    plot(bnr.abd, dpos=c(105, 100))
    bnr.abd$n <- 26
    # To identify a point on the graph, use: bnr.abd$n <- identify(bnr.abd)
    lines(bnr.abd)
    bnr2 <- extract(bnr.abd)
    names(bnr2)

[Package pastecs version 1.3-2 Index]